It works! Thank you so much for this! I hope that in the future an installation package including all these softwares can be available for GUI users and when a new version of one software is available, what we need to do is only to click the mouse to update it. Thank you again. Best, Shun On Jan 6, 2015, at 3:42 PM, Nathaniel Echols wrote:

Check your settings in the Phenix preferences (Graphics section) - does this have an explicit path to Coot set? If so, you will probably need to update it. (In the future, it would probably be worth having Phenix include ccp4 installations in the automatic detection, but that still won't fix the problem if a specific path is set in the preferences.)

On Tue, Jan 6, 2015 at 3:38 PM, Shun Liu wrote: Dear all,

After I updated ccp4 to a new version (ccp4-6.5), I found that coot failed to launch in phenix.

/Applications/PHENIX-1.9-1692/Contents/phenix-1.9-1692/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/start_coot.sh: line 37: /Applications/ccp4-6.4.0/coot.app/Contents/MacOS/coot: No such file or directory

Apparently it requires ccp4-6.4.0, which has been deleted. I tried to modify find_coot_command.py in phenix, but it didn’t work. Can anybody give me some suggestions so that I can figure this problem out? Thanks!

Best,

Shun

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Thanks to contributions of developers including you, today it becomes easier for most GUI users with little compiling skill to use these free GUI softwares and I can feel the change. Hope for a better tomorrow. Thanks! Best, Shun On Jan 6, 2015, at 4:27 PM, Nathaniel Echols wrote:

On Tue, Jan 6, 2015 at 4:01 PM, Shun Liu wrote: It works! Thank you so much for this! I hope that in the future an installation package including all these softwares can be available for GUI users and when a new version of one software is available, what we need to do is only to click the mouse to update it. Thank you again.

Most of these programs are under restrictive licenses which limit their distribution. (Coot is the big exception, but it's also even messier to build than Phenix.) If you want an integrated solution, I urge you to look into joining SBGrid, which takes care of all building/installation issues and will automatically push out updates as they become available. (This is done on a per-lab basis but I have also seen individual laptops set up as SBgrid clients.) The disadvantages are (1) it costs money, and (2) it may not always update as quickly as you'd like - looks like they haven't switched to CCP4 6.5 yet but I assume this is what happens when you release software right before Christmas. But I think it is a huge improvement over the old system where random grad students got stuck handling system administration and arcane software. It has certainly simplified Phenix support, especially where Rosetta integration is concerned.

(In any case, I have modified the script that auto-detects Coot installations so that it will also check for CCP4 installations on Mac - and pick the newest one containing Coot - so you won't have to enter this in the preferences any more.)

Just be glad you're doing crystallography and not next-gen sequencing - programs like Phenix/CCP4/Coot are vastly simpler to install and use, and there's much less fragmentation of developer efforts (especially since everyone has standardized on Coot for interactive model-building).

-Nat